Encyclopedia of Metagenomics

2015 Edition
| Editors: Sarah K. Highlander, Francisco Rodriguez-Valera, Bryan A. White

Complex Indoor Communities: Bacterial Life Under Extreme Conditions in Clean Rooms and Intensive Care Units

  • Lisa Oberauner
  • Alexander Mahnert
  • Anastasia Bragina
  • Gabriele Berg
Reference work entry
DOI: https://doi.org/10.1007/978-1-4899-7475-4_322


Microbiome of built environments


Indoor microbiomes are communities of microorganisms that inhabit the interior of built environments and are influenced by complex abiotic (e.g., climate, geographic location, building architecture, and maintenance) and biotic factors (human and animals/pets dynamics, greenery status, etc.).

Introduction to Indoor Microbiomes

Although microbes have often been recognized as pathogens, it is now well established that the majority of host-bacterial interactions are symbiotic (Blaser 2011). This partnership is based on molecular signaling to mediate beneficial outcomes for both microbes and their hosts. This relationship between microbial diversity and host health was shown not only for plants and soils but also for animals and humans (Keesing et al. 2010). Despite the fact that the majority of our lifetime is spent in indoor environments such as the home, workplace, or public buildings (Fig. 1, Table 1), our knowledge of microbial...
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  1. Blaser M. Antibiotic overuse: stop the killing of beneficial bacteria. Nature. 2011;476:393–4.PubMedGoogle Scholar
  2. Dunn RR, Fierer N, Henley JB, et al. Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes. PLoS ONE. 2013;8(5):e64133.PubMedCentralPubMedGoogle Scholar
  3. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A. 2008;105:17994–9.PubMedCentralPubMedGoogle Scholar
  4. Flores GE, Bates ST, Knights D, et al. Microbial biogeography of public restroom surfaces. PLoS ONE. 2011;6:e28132.PubMedCentralPubMedGoogle Scholar
  5. Flores GE, Bates ST, Caporaso JG, et al. Diversity, distribution and sources of bacteria in residential kitchens. Environ Microbiol. 2013;15:588–96.PubMedGoogle Scholar
  6. Hanski I, von Hertzen L, Fyhrquist N, et al. Environmental biodiversity, human microbiota, and allergy are interrelated. Proc Natl Acad Sci U S A. 2012;109:8334–9.PubMedCentralPubMedGoogle Scholar
  7. Hewitt KM, Gerba CP, Maxwell SL, Kelley ST. Office space bacterial abundance and diversity in three metropolitan areas. PLoS ONE. 2012;7:e37849.PubMedCentralPubMedGoogle Scholar
  8. Hewitt KM, Mannino FL, Gonzalez A, et al. Bacterial diversity in two Neonatal Intensive Care Units (NICUs). PLoS ONE. 2013;8:e54703.PubMedCentralPubMedGoogle Scholar
  9. Keesing F, Belden LK, Daszak P, et al. Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature. 2010;468:647–52.PubMedGoogle Scholar
  10. Kelley ST, Gilbert JA. Studying the microbiology of the indoor environment. Genome Biol. 2013;14:202.PubMedCentralPubMedGoogle Scholar
  11. Kembel SW, Jones E, Kline J, et al. Architectural design influences the diversity and structure of the built environment microbiome. ISME J. 2012;6:1469–79.PubMedCentralPubMedGoogle Scholar
  12. Kramer A, Schwebke I, Kampf G. How long do nosocomial pathogens persist on inanimate surfaces? A systematic review. BMC Infect Dis. 2006;6:130.PubMedCentralPubMedGoogle Scholar
  13. La Duc MT, Dekas A, Osman S, et al. Isolation and characterization of bacteria capable of tolerating the extreme conditions of clean room environments. Appl Environ Microbiol. 2007;73:2600–11.PubMedCentralPubMedGoogle Scholar
  14. Moissl C, Osman S, La Duc MT, et al. Molecular bacterial community analysis of clean rooms where spacecraft are assembled. FEMS Microbiol Ecol. 2007;61:509–21.PubMedGoogle Scholar
  15. Moissl-Eichinger C. Archaea in artificial environments: their presence in global spacecraft clean rooms and impact on planetary protection. ISME J. 2011;5:209–19.PubMedCentralPubMedGoogle Scholar
  16. Oberauner L, Zachow C, Lackner S, et al. The ignored diversity: complex bacterial communities in intensive care units revealed by 16S pyrosequencing. Sci Rep. 2013;3:1413.PubMedCentralPubMedGoogle Scholar
  17. Pitkäranta M, Meklin T, Hyvärinen A, et al. Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture. Appl Environ Microbiol. 2008;74:233–44.PubMedCentralPubMedGoogle Scholar
  18. Plowman R. The socioeconomic burden of hospital acquired infection. Euro Surveill. 2000;5:49–50.PubMedGoogle Scholar
  19. Qian J, Hospodsky D, Yamamoto N, et al. Size-resolved emission rates of airborne bacteria and fungi in an occupied class room. Indoor Air. 2012;22:339–51.PubMedCentralPubMedGoogle Scholar
  20. Vaishampayan P, Probst AJ, La Duc MT, et al. New perspectives on viable microbial communities in low-biomass cleanroom environments. ISME J. 2013;7:312–24.PubMedCentralPubMedGoogle Scholar
  21. Wagner AO, Malin C, Knapp BA, Illmer P. Removal of free extracellular DNA from environmental samples by ethidium monoazide and propidium monoazide. Appl Environ Microbiol. 2008;74:2537–9.PubMedCentralPubMedGoogle Scholar
  22. Yamamoto N, Shendell DG, Peccia J. Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air. 2011;21:521–530.PubMedGoogle Scholar
  23. Zalar P, Novak M, De Hoog GS, et al. Dishwashers—a man-made ecological niche accommodating human opportunistic fungal pathogens. Fungal Biol. 2011;115:997–1007.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Lisa Oberauner
    • 1
    • 2
  • Alexander Mahnert
    • 2
  • Anastasia Bragina
    • 2
  • Gabriele Berg
    • 2
  1. 1.Austrian Centre of Industrial Biotechnology (ACIB GmbH)GrazAustria
  2. 2.Institute of Environmental Biotechnology, Graz University of TechnologyGrazAustria